Figure 3. The rise in the proportion of non-synonymous sites in Europeans compared with West Africans is not due to a reduced effectiveness of selection in Europeans since the split.

(A) The West African and European diploid population sizes for the two simulated models (left, ref. ⁶, and right, a bottleneck followed by expansion), both of which specify a population split 2,040 generations ago. Subsequent panels are restricted to Europeans, as the West African population size does not fluctuate enough to cause statistics to deviate substantially from the baseline. (B) Key statistics as a fraction of the baseline. The present proportion of non-synonymous sites in Europeans is higher than in the ancestral population (black). We also show heterozygosity at unselected sites (gray), synonymous site density (red), and non-synonymous site density (yellow). (C) Partitioning of the change in the proportion of non-synonymous sites per generation into selective and others forces. For both models, the temporal dynamics are driven by the forces of mutation and stochastic changes in allele frequency (the curves are positively correlated) and not by negative selective forces (negatively correlated). We plot the per-generation change in the proportion of non-synonymous mutations due to selection minus its value prior to the West African / European population split used as a baseline. A positive value does not mean that selection is working to increase the proportion of non-synonymous mutations, just that the decrease per generation due to this quantity is less than in the past.